You should probably look into why framing changes so much when guiding stops during focus. Autofocus works much better when PHD2 isn't fighting against it. I always have guiding turned off during autofocus. I do get a slight amount of image shift, but I set the search region in PHD2 to be the largest allowed and the guide star always stays inside the box during AF, and when guiding resumes, PHD2 will bring the guide star back to its original position.
Tim